Biology subjects

Sorre, B.

Publications and source records attributed to Sorre, B..

7 recordsLinked to original sources

bioRxiv2025

Morphogen gradients applied basally to human embryonic stem cells to control and dissect tissue patterning

Morphogen gradients are used repeatedly during development to pattern embryonic tissues. Absolute concentrations, duration or even temporal derivative of morphogen concentration have all been proposed to carry positional information. However, establishing the causal relationship between the gradient spatio-temporal profile and resulting cellular diversity and tissue patterning is difficult to address in live embryos because of lack of tools to control those variables. Here, we developed microfluidics devices able to apply spatio-temporally well-defined morphogen landscapes on the basal side of human embryonic stem cells colonies, thus mimicking how BMP4 is delivered to the pluripotent epiblast during mouse gastrulation. Combining live imaging and theoretical modelling, we show that in this configuration the absolute concentration of BMP4 provides positional information and the cell identities emerging during differentiation can vary according to the shape of the gradient. Our toolbox provides a powerful means to dissect the logic of patterning and to engineer tissues precisely.

developmental biology↗

bioRxiv2024

BMP signaling modulations control primitive streak patterning

The primitive streak (PS) is the embryonic structure from which mesoderm and definitive endoderm cells emerge to form organs and fetal tissues. The identities of the cells leaving the PS depend on both the time and the position at which they exit. Three signaling molecules, BMP4, WNT3 and NODAL, play key roles in determining these identities, but it has been difficult to disentangle the contribution of each to this process in the mouse embryo. Using 2D gastruloids that recapitulate early aspects of mouse gastrulation in vitro, we have previously shown that WNT3 and NODAL promote distal PS fates on their own, and proximal PS fates in the presence of BMP4. We now detail further the impact of BMP4 on the cell identities produced in gastruloids. Single cell RNA-seq analysis shows that prolonged exposure to BMP4 results in the presence of all the cell types, including primordial germ cells, which normally form from the most proximal part of the pluripotent epiblast. We then show that reducing the duration or intensity of gastruloid exposure to BMP4 can allow the emergence of more distal cell identities, such as paraxial mesoderm, alongside anterior PS derivatives. These results, which are consistent with embryological studies, provide key elements for understanding how the varied output of the PS is controlled.

developmental biology↗

bioRxiv2023

Optogenetic spatial patterning of cooperation in yeast populations

Microbial communities are a siege of complex metabolic interactions such as cooperation and competition for resources. Methods to control such interactions could lead to major advances in our ability to engineer microbial consortia for bioproduction and synthetic biology applications. Here, we used optogenetics to control invertase production in yeast, thereby creating landscapes of cooperator and cheater cells. Yeast cells behave as cooperators (i.e., transform sucrose into glucose, a public "good") upon blue light illumination or cheaters (i.e., consume glucose produced by cooperators to grow) in the dark. We show that cooperators benefit best from the hexoses they produce when their domain size is constrained between two cut-off length-scales. From an engineering point of view, the system behaves as a band pass filter. The lower limit is the trace of cheaters competition for hexoses, while the upper limit is defined by cooperators competition for sucrose. Hence, cooperation mostly occurs at the frontiers with cheater cells, which not only compete for hexoses but also cooperate passively by letting sucrose reach cooperators. We anticipate that this optogenetic method could be applied to shape metabolic interactions in a variety of microbial ecosystems.

synthetic biology↗

bioRxiv2023

Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability

Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.

systems biology↗

bioRxiv2022

Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales

Optogenetics arises as a valuable tool to precisely control genetic circuits in microbial cell factories. Light control holds the promise of optimizing bioproduction methods and maximize yields, but its implementation at different steps of the strain development process and at different culture scales remains challenging. In this study, we aim to control beta-carotene bioproduction using optogenetics in Saccharomyces cerevisiae and investigate how its performance translates across culture scales. We built four lab-scale illumination devices, each handling different culture volumes, and each having specific illumination characteristics and cultivating conditions. We evaluated optogenetic activation and beta-carotene production across devices and optimized them both independently. Then, we combined optogenetic induction and beta-carotene production to make a light-inducible beta-carotene producer strain. This was achieved by placing the transcription of the bifunctional lycopene cyclase / phytoene synthase CrtYB under the control of the pC120 optogenetic promoter regulated by the EL222-VP16 light-activated transcription factor, while other carotenogenic enzymes (CrtI, CrtE, tHMG) were expressed constitutively. We show that illumination, culture volume and shaking impact differently optogenetic activation and beta-carotene production across devices. This enabled us to determine the best culture conditions to maximize light-induced beta-carotene production in each of the devices, reaching a content of up to 880 g/gCDW. Our study exemplifies the stakes of scaling up optogenetics in devices of different lab scales and sheds light on the interplays and potential conflicts between optogenetic control and metabolic pathway efficiency. As a general principle, we propose that it is important to first optimize both components of the system independently, before combining them into optogenetic producing strains to avoid extensive troubleshooting. We anticipate that our results can help designing both strains and devices that could eventually lead to larger scale systems in an effort to bring optogenetics to the industrial scale.

synthetic biology↗

bioRxiv2022

CyberSco.Py: open-source software for event-based, conditional microscopy

Timelapse fluorescence microscopy imaging is routinely used in quantitative cell biology. However, microscopes could become much more powerful investigation systems if they were endowed with simple unsupervised decision-making algorithms to transform them into fully responsive and automated measurement devices. Here, we report CyberSco.Py, Python software for advanced automated timelapse experiments. We provide proof-of-principle of a user-friendly framework that increases the tunability and flexibility when setting up and running fluorescence timelapse microscopy experiments. Importantly, CyberSco.Py combines real-time image analysis with automation capability, which allows users to create conditional, event-based experiments in which the imaging acquisition parameters and the status of various devices can be changed automatically based on the image analysis. We exemplify the relevance of CyberSco.Py to cell biology using several use case experiments with budding yeast. We anticipate that CyberSco.Py could be used to address the growing need for smart microscopy systems to implement more informative quantitative cell biology experiments.

cell biology↗

bioRxiv2020

Dissecting signalling hierarchies in the patterning of the mouse primitive streak using micro-patterned EpiLC colonies.

Molecular embryology studies have established that the patterning of the gastrula-stage mouse embryo is dependent on a regulatory network where the WNT, BMP and NODAL signalling pathways cooperate. Still, important aspects of their respective contributions to this process remain unclear. Here, studying their impact on the spatial organization and the developmental trajectories of micro-patterned Epiblast Like Cells (EpiLC) colonies, we show that when BMP is present, it dominates NODAL and WNT and imposes a posterior character to the colonies differentiation. However, the use of two Nodal mutant cell lines allowed us to show that prior to BMP action, NODAL is required to establish the mesendodermal lineage. The fact that mutant phenotypes were more severe in vitro than in vivo suggests that embryonic phenotypes are partially rescued by ligands of extra-embryonic or maternal origin. Our work demonstrates the complementarity of micro-patterned EpiLC colonies to embryological approaches.

developmental biology↗